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- EMDB-31251: Overall structure of Erastin-bound xCT-4F2hc complex -

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Basic information

Entry
Database: EMDB / ID: EMD-31251
TitleOverall structure of Erastin-bound xCT-4F2hc complex
Map data
Sample
  • Complex: Overall structure of Erastin-bound xCT-4F2hc complex
    • Protein or peptide: 4F2 cell-surface antigen heavy chain
    • Protein or peptide: Cystine/glutamate transporter
  • Ligand: 2-[(1S)-1-[4-[2-(4-chloranylphenoxy)ethanoyl]piperazin-1-yl]ethyl]-3-(2-ethoxyphenyl)quinazolin-4-one
  • Ligand: 1,2-DISTEAROYL-SN-GLYCERO-3-PHOSPHATE
KeywordsMEMBRANE PROTEIN
Function / homology
Function and homology information


cystine:glutamate antiporter activity / regulation of neutrophil apoptotic process / L-kynurenine transmembrane transport / L-kynurenine transmembrane transporter activity / regulation of cysteine metabolic process / regulation of glutathione biosynthetic process / regulation of glutamate metabolic process / regulation of melanin biosynthetic process / regulation of AMPA glutamate receptor clustering / L-cystine transport ...cystine:glutamate antiporter activity / regulation of neutrophil apoptotic process / L-kynurenine transmembrane transport / L-kynurenine transmembrane transporter activity / regulation of cysteine metabolic process / regulation of glutathione biosynthetic process / regulation of glutamate metabolic process / regulation of melanin biosynthetic process / regulation of AMPA glutamate receptor clustering / L-cystine transport / Defective SLC7A7 causes lysinuric protein intolerance (LPI) / neutral L-amino acid secondary active transmembrane transporter activity / apical pole of neuron / aromatic amino acid transmembrane transporter activity / tyrosine transport / L-histidine transport / amino acid transport complex / dipeptide import across plasma membrane / L-leucine import across plasma membrane / L-alanine transmembrane transporter activity / L-alanine import across plasma membrane / regulation of protein transport / isoleucine transport / phenylalanine transport / methionine transport / L-amino acid transmembrane transporter activity / valine transport / L-leucine transmembrane transporter activity / calcium:sodium antiporter activity / L-leucine transport / thyroid hormone transport / proline transport / L-glutamate transmembrane transport / glutathione transmembrane transport / amino acid transmembrane transport / regulation of cellular response to oxidative stress / ventricular system development / lens fiber cell differentiation / intracellular glutamate homeostasis / Amino acid transport across the plasma membrane / neutral L-amino acid transmembrane transporter activity / L-glutamate import across plasma membrane / Tryptophan catabolism / striatum development / astrocyte projection / exogenous protein binding / anchoring junction / limb development / Basigin interactions / negative regulation of ferroptosis / response to redox state / microvillus membrane / NFE2L2 regulating anti-oxidant/detoxification enzymes / lung alveolus development / amino acid transport / regulation of synapse organization / adult behavior / response to exogenous dsRNA / tryptophan transport / glutathione metabolic process / basal plasma membrane / response to nicotine / brush border membrane / modulation of chemical synaptic transmission / visual learning / response to organic cyclic compound / platelet aggregation / response to toxic substance / calcium ion transport / double-stranded RNA binding / melanosome / apical part of cell / virus receptor activity / regulation of cell population proliferation / cellular response to oxidative stress / basolateral plasma membrane / carbohydrate metabolic process / cadherin binding / symbiont entry into host cell / protein heterodimerization activity / apical plasma membrane / lysosomal membrane / synapse / cell surface / protein homodimerization activity / RNA binding / extracellular exosome / nucleoplasm / membrane / plasma membrane
Similarity search - Function
L-type amino acid transporter / Solute carrier family 3 member 2, N-terminal domain / 4F2 cell-surface antigen heavy chain / Solute carrier family 3 member 2 N-terminus / : / Amino acid/polyamine transporter I / Amino acid permease / Alpha amylase, catalytic domain / Glycosyl hydrolase, family 13, catalytic domain / Alpha-amylase domain ...L-type amino acid transporter / Solute carrier family 3 member 2, N-terminal domain / 4F2 cell-surface antigen heavy chain / Solute carrier family 3 member 2 N-terminus / : / Amino acid/polyamine transporter I / Amino acid permease / Alpha amylase, catalytic domain / Glycosyl hydrolase, family 13, catalytic domain / Alpha-amylase domain / Glycosyl hydrolase, all-beta / Glycoside hydrolase superfamily
Similarity search - Domain/homology
Amino acid transporter heavy chain SLC3A2 / Cystine/glutamate transporter
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.4 Å
AuthorsYan RH / Li YN
Funding support China, 3 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31971123 China
National Natural Science Foundation of China (NSFC)81920108015 China
National Natural Science Foundation of China (NSFC)31930059 China
CitationJournal: Cell Res / Year: 2022
Title: The structure of erastin-bound xCT-4F2hc complex reveals molecular mechanisms underlying erastin-induced ferroptosis.
Authors: Renhong Yan / Enjun Xie / Yaning Li / Jin Li / Yuanyuan Zhang / Ximin Chi / Xueping Hu / Lei Xu / Tingjun Hou / Brent R Stockwell / Junxia Min / Qiang Zhou / Fudi Wang /
History
DepositionApr 28, 2021-
Header (metadata) releaseApr 6, 2022-
Map releaseApr 6, 2022-
UpdateOct 30, 2024-
Current statusOct 30, 2024Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_31251.png

Downloads & links

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Map

FileDownload / File: emd_31251.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.09 Å/pix.
x 256 pix.
= 278.272 Å		1.09 Å/pix.
x 256 pix.
= 278.272 Å		1.09 Å/pix.
x 256 pix.
= 278.272 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.087 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.03
Minimum - Maximum-0.08897332 - 0.14987972
Average (Standard dev.)-0.00006254848 (±0.0040526595)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 278.272 Å
α=β=γ: 90.0 °

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Supplemental data

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Sample components

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Entire : Overall structure of Erastin-bound xCT-4F2hc complex

EntireName: Overall structure of Erastin-bound xCT-4F2hc complex
Components
  • Complex: Overall structure of Erastin-bound xCT-4F2hc complex
    • Protein or peptide: 4F2 cell-surface antigen heavy chain
    • Protein or peptide: Cystine/glutamate transporter
  • Ligand: 2-[(1S)-1-[4-[2-(4-chloranylphenoxy)ethanoyl]piperazin-1-yl]ethyl]-3-(2-ethoxyphenyl)quinazolin-4-one
  • Ligand: 1,2-DISTEAROYL-SN-GLYCERO-3-PHOSPHATE

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Supramolecule #1: Overall structure of Erastin-bound xCT-4F2hc complex

SupramoleculeName: Overall structure of Erastin-bound xCT-4F2hc complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: 4F2 cell-surface antigen heavy chain

MacromoleculeName: 4F2 cell-surface antigen heavy chain / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 70.160828 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MAHHHHHHHH HHSGRELQPP EASIAVVSIP RQLPGSHSEA GVQGLSAGDD SETGSDCVTQ AGLQLLASSD PPALASKNAE VTVETGFHH VSQADIEFLT SIDPTASASG SAGITGTMSQ DTEVDMKEVE LNELEPEKQP MNAASGAAMS LAGAEKNGLV K IKVAEDEA ...String:
MAHHHHHHHH HHSGRELQPP EASIAVVSIP RQLPGSHSEA GVQGLSAGDD SETGSDCVTQ AGLQLLASSD PPALASKNAE VTVETGFHH VSQADIEFLT SIDPTASASG SAGITGTMSQ DTEVDMKEVE LNELEPEKQP MNAASGAAMS LAGAEKNGLV K IKVAEDEA EAAAAAKFTG LSKEELLKVA GSPGWVRTRW ALLLLFWLGW LGMLAGAVVI IVRAPRCREL PAQKWWHTGA LY RIGDLQA FQGHGAGNLA GLKGRLDYLS SLKVKGLVLG PIHKNQKDDV AQTDLLQIDP NFGSKEDFDS LLQSAKKKSI RVI LDLTPN YRGENSWFST QVDTVATKVK DALEFWLQAG VDGFQVRDIE NLKDASSFLA EWQNITKGFS EDRLLIAGTN SSDL QQILS LLESNKDLLL TSSYLSDSGS TGEHTKSLVT QYLNATGNRW CSWSLSQARL LTSFLPAQLL RLYQLMLFTL PGTPV FSYG DEIGLDAAAL PGQPMEAPVM LWDESSFPDI PGAVSANMTV KGQSEDPGSL LSLFRRLSDQ RSKERSLLHG DFHAFS AGP GLFSYIRHWD QNERFLVVLN FGDVGLSAGL QASDLPASAS LPAKADLLLS TQPGREEGSP LELERLKLEP HEGLLLR FP YAALE

UniProtKB: Amino acid transporter heavy chain SLC3A2

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Macromolecule #2: Cystine/glutamate transporter

MacromoleculeName: Cystine/glutamate transporter / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 57.609777 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MADYKDDDDK SGPDEVDASG RVRKPVVSTI SKGGYLQGNV NGRLPSLGNK EPPGQEKVQL KRKVTLLRGV SIIIGTIIGA GIFISPKGV LQNTGSVGMS LTIWTVCGVL SLFGALSYAE LGTTIKKSGG HYTYILEVFG PLPAFVRVWV ELLIIRPAAT A VISLAFGR ...String:
MADYKDDDDK SGPDEVDASG RVRKPVVSTI SKGGYLQGNV NGRLPSLGNK EPPGQEKVQL KRKVTLLRGV SIIIGTIIGA GIFISPKGV LQNTGSVGMS LTIWTVCGVL SLFGALSYAE LGTTIKKSGG HYTYILEVFG PLPAFVRVWV ELLIIRPAAT A VISLAFGR YILEPFFIQC EIPELAIKLI TAVGITVVMV LNSMSVSWSA RIQIFLTFCK LTAILIIIVP GVMQLIKGQT QN FKDAFSG RDSSITRLPL AFYYGMYAYA GWFYLNFVTE EVENPEKTIP LAICISMAIV TIGYVLTNVA YFTTINAEEL LLS NAVAVT FSERLLGNFS LAVPIFVALS CFGSMNGGVF AVSRLFYVAS REGHLPEILS MIHVRKHTPL PAVIVLHPLT MIML FSGDL DSLLNFLSFA RWLFIGLAVA GLIYLRYKCP DMHRPFKVPL FIPALFSFTC LFMVALSLYS DPFSTGIGFV ITLTG VPAY YLFIIWDKKP RWFRIMSEKI TRTLQIILEV VPEEDKL

UniProtKB: Cystine/glutamate transporter

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Macromolecule #4: 2-[(1S)-1-[4-[2-(4-chloranylphenoxy)ethanoyl]piperazin-1-yl]ethyl...

MacromoleculeName: 2-[(1S)-1-[4-[2-(4-chloranylphenoxy)ethanoyl]piperazin-1-yl]ethyl]-3-(2-ethoxyphenyl)quinazolin-4-one
type: ligand / ID: 4 / Number of copies: 1 / Formula: J9O
Molecular weightTheoretical: 547.045 Da
Chemical component information

ChemComp-J9O:
2-[(1S)-1-[4-[2-(4-chloranylphenoxy)ethanoyl]piperazin-1-yl]ethyl]-3-(2-ethoxyphenyl)quinazolin-4-one

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Macromolecule #5: 1,2-DISTEAROYL-SN-GLYCERO-3-PHOSPHATE

MacromoleculeName: 1,2-DISTEAROYL-SN-GLYCERO-3-PHOSPHATE / type: ligand / ID: 5 / Number of copies: 2 / Formula: PX8
Molecular weightTheoretical: 703.99 Da
Chemical component information

ChemComp-PX8:
1,2-DISTEAROYL-SN-GLYCERO-3-PHOSPHATE

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 8
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.2 µm / Nominal defocus min: 1.2 µm
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: OTHER
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.0.6) / Number images used: 114524
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: MAXIMUM LIKELIHOOD

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